Comparative genomic analysis of the Streptococcus dysgalactiae species group: Gene content, molecular adaptation, and promoter evolution

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 168-185

  Suzuki, Haruo ^a   Lefébure, Tristan ^a,c,d   Hubisz, Melissa Jane ^b   Bitar, Paulina Pavinski ^a   Lang, Ping ^a   Siepe, Adam ^b   Stanhope, Michael J ^a  

^a Department of Obstetrics Gynecology   (United States)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c UNIVERSITÉ DE LYON   (France)

^d UNIVERSITÉ LYON 1   (France)

Author keywords

Gene content; Molecular adaptation; Promoter evolution; S. dysgalactiae subsp. dysgalactiae; Streptococcus dysgalactiae subsp. equisimilis

Indexed keywords

ANIMALIA; BACTERIA (MICROORGANISMS); STREPTOCOCCUS; STREPTOCOCCUS DYSGALACTIAE; STREPTOCOCCUS DYSGALACTIAE SUBSP. DYSGALACTIAE; STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUISIMILIS;

BACTERIAL PROTEIN;

ANIMAL; ANIMAL DISEASE; ARTICLE; BACTERIAL GENOME; CATTLE; CATTLE DISEASE; CHEMISTRY; CHILD; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; GENOMICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PROMOTER REGION; STREPTOCOCCUS; STREPTOCOCCUS INFECTION;

ANIMALS; BACTERIAL PROTEINS; CATTLE; CATTLE DISEASES; CHILD; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROMOTER REGIONS, GENETIC; STREPTOCOCCAL INFECTIONS; STREPTOCOCCUS;

EID: 79958283181     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr006     Document Type: Article

References (84)

1. Abdelsalam M, Chen SC, Yoshida T. 2010. Dissemination of streptococcal pyrogenic exotoxin G (spegg) with an IS-like element in fish isolates of Streptococcus dysgalactiae. FEMS Microbiol Lett. 309:105-113.
2. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
3. Andolfatto P. 2005. Adaptive evolution of non-coding DNA inDrosophila. Nature 437:1149-1152. (Pubitemid 41509351)
4. Arakawa K, et al. 2003. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19:305-306. (Pubitemid 36181925)
5. Arakawa K, Tomita M. 2006. G-language System as a platform for largescale analysis of high-throughput omics data. J Pesticide Sci. 31:282-288. (Pubitemid 44285776)
6. Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29. (Pubitemid 30257031)
7. Benjamini Y, Yekutieli D. 2001. The control of the false discovery rate in multiple testing under dependency. Ann Statist. 29:1165-1188. (Pubitemid 33575263)
8. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2009. GenBank. Nucleic Acids Res. 37:D26-D31.
9. Bergmann S, et al. 2003. Identification of a novel plasmin(ogen)-binding motif in surface displayed alpha-enolase of Streptococcus pneumoniae. Mol Microbiol. 49:411-423. (Pubitemid 36851197)
10. Bert F, Branger C, Poutrel B, Lambert-Zechovsky N. 1997. Differentiation of human and animal strains of Streptococcus dysgalactiae by pulsed-field gel electrophoresis. FEMS Microbiol Lett. 150:107-112. (Pubitemid 27234420)
11. Blanchette M, et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14:708-715. (Pubitemid 38500244)
12. Bourgoin F, Pluvinet A, Gintz B, Decaris B, Guedon G. 1999. Are horizontal transfers involved in the evolution of the Streptococcus thermophilus exopolysaccharide synthesis loci? Gene 233:151-161. (Pubitemid 29353234)
13. Brady LJ, Piacentini DA, Crowley PJ, Oyston PC, Bleiweis AS. 1992. Differentiation of salivary agglutinin-mediated adherence and aggregation of mutans streptococci by use of monoclonal antibodies against the major surface adhesin P1. Infect Immun. 60:1008-1017.
14. Brandt CM, Spellerberg B. 2009. Human infections due to Streptococcus dysgalactiae subspecies equisimilis. Clin Infect Dis. 49:766-772.
15. Brochet M, Couve E, Glaser P, Guedon G, Payot S. 2008. Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae. J Bacteriol. 190:6913-6917.
16. Chen L, et al. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33:D325-D328. (Pubitemid 40207888)
17. Chenier S, Leclere M, Messier S, Fecteau G. 2008. Streptococcus dysgalactiae cellulitis and toxic shock like syndrome in a Brown Swiss cow. J Vet Diagn Invest. 20:99-103. (Pubitemid 352843953)
18. Churchward G. 2007. The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci. Mol Microbiol. 64:34-41. (Pubitemid 46435042)
19. Davidsen T, et al. 2010. The comprehensive microbial resource. Nucleic Acids Res. 38:D340-D345.
20. Davies MR, et al. 2007. Virulence profiling of Streptococcus dysgalactiae subspecies equisimilis isolated from infected humans reveals 2 distinct genetic lineages that do not segregate with their phenotypes or propensity to cause diseases. Clin Infect Dis. 44:1442-1454. (Pubitemid 46801587)
21. Davies MR, Shera J, Van Domselaar GH, Sriprakash KS, McMillan DJ. 2009. A novel integrative conjugative element mediates genetic transfer from group G Streptococcus to other {beta}-hemolytic Streptococci. J Bacteriol. 191:2257-2265.
22. Demers B, et al. 1993. Severe invasive group A streptococcal infections in Ontario, Canada: 1987-1991. Clin Infect Dis. 16:792-800 discussion 801-792. (Pubitemid 23157983)
23. Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74. (Pubitemid 30056993)
24. Ferretti JJ, et al. 2001. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A. 98:4658-4663. (Pubitemid 32295032)
25. Gardner PP, et al. 2009. Rfam: updates to the RNA families database. Nucleic Acids Res. 37:D136-D140.
26. Glazunova OO, Raoult D, Roux V. 2010. Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus. Int J Syst Evol Microbiol. 60:2140-2148.
27. Grant JR, Stothard P. 2008. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36:W181-W184.
28. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
29. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704. (Pubitemid 37365050)
30. Haenni M, et al. 2010. Diversity and mobility of integrative andconjugative elements in bovine isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis. Appl Environ Microbiol. 76:7957-7965.
31. Hashikawa S, et al. 2004. Characterization of group C and G streptococcal strains that cause streptococcal toxic shock syndrome. J Clin Microbiol. 42:186-192. (Pubitemid 38082718)
32. Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet. 39:1140-1144. (Pubitemid 47340653)
33. Heather Z, et al. 2008. A novel streptococcal integrative conjugative element involved in iron acquisition. Mol Microbiol. 70:1274-1292.
34. Henry I, Sharp PM. 2007. Predicting gene expression level from codon usage bias. Mol Biol Evol. 24:10-12. (Pubitemid 46026275)
35. Holden MT, et al. 2009. Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One 4:e6072.
36. Holm SE, Norrby A, Bergholm AM, Norgren M. 1992. Aspects of pathogenesis of serious group A streptococcal infections in Sweden, 1988-1989. J Infect Dis. 166:31-37.
37. Hsueh PR, et al. 1998. Invasive group A streptococcal disease in Taiwan is not associated with the presence of streptococcal pyrogenic exotoxin genes. Clin Infect Dis. 26:584-589.
38. Karlin S, Mrazek J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol. 182:5238-5250.
39. Karp PD, et al. 2009. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 11:40-79.
40. Kazakov AE, et al. 2007. RegTransBase-a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 35:D407-D412. (Pubitemid 46056241)
41. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 100:11484-11489. (Pubitemid 37205962)
42. Kent WJ, et al. 2002. The human genome browser at UCSC. Genome Res. 12:996-1006.
43. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096-3098. (Pubitemid 44884087)
44. Kosiol C, et al. 2008. Patterns of positive selection in six Mammalian genomes. PLoS Genet 4:e1000144.
45. Kreikemeyer B, McIver KS, Podbielski A. 2003. Virulence factor regulation and regulatory networks in Streptococcus pyogenes and their impact on pathogen-host interactions. Trends Microbiol. 11:224-232. (Pubitemid 36645006)
46. Laus F, et al. 2007. Clinical and epidemiological investigation of chronic upper respiratory diseases caused by beta-haemolytic Streptococci in horses. Comp Immunol Microbiol Infect Dis. 30:247-260. (Pubitemid 46825178)
47. Lefé bure T, Stanhope MJ. 2007. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8:R71.
48. Lefé bure T, Stanhope MJ. 2009. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus. Campylobacter Genome Res. 19:1224-1232.
49. Leplae R, Lima-Mendez G, Toussaint A. 2010. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 38:D57-D61.
50. Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189. (Pubitemid 37161775)
51. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. 2008. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24:863-865. (Pubitemid 351386927)
52. Lobry JR. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 13:660-665. (Pubitemid 26131887)
53. Lowe BA, Miller JD, Neely MN. 2007. Analysis of the polysaccharide capsule of the systemic pathogen Streptococcus iniae and its implications in virulence. Infect Immun. 75:1255-1264. (Pubitemid 46385817)
54. Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet. 11:181-190.
55. McDonald TJ, McDonald JS. 1976. Streptococci isolated from bovine intramammary infections. Am J Vet Res. 37:377-381.
56. McShan WM, et al. 2008. Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. J Bacteriol. 190:7773-7785.
57. Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. 2008. Genome- Matcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 9:376.
58. Panchaud A, et al. 2009. M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island. BMC Genomics 10:198.
59. Pavlovic G, Burrus V, Gintz B, Decaris B, Guedon G. 2004. Evolution of genomic islands by deletion and tandem accretion by site-specificrecombination: ICE St1-related elements from Streptococcus thermophilus. Microbiology 150:759-774. (Pubitemid 38523295)
60. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20:110-121.
61. Proft T, Sriskandan S, Yang L, Fraser JD. 2003. Superantigens and streptococcal toxic shock syndrome. Emerg Infect Dis. 9:1211-1218. (Pubitemid 37210560)
62. R-Development-Core-Team. 2010. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
63. Rhead B, et al. 2010. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38:D613-D619.
64. Rolston KV. 1986. Group G streptococcal infections. Arch Intern Med. 146:857-858. (Pubitemid 16116656)
65. Roshan U, Livesay DR. 2006. Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22:2715-2721. (Pubitemid 44742389)
66. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33:1141-1153. (Pubitemid 41439907)
67. Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050. (Pubitemid 41126859)
68. Siepel A, Haussler D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488. (Pubitemid 38339664)
69. Stothard P, Wishart DS. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539. (Pubitemid 40310241)
70. Sun H, et al. 2004. Plasminogen is a critical host pathogenicity factor for group A streptococcal infection. Science 305:1283-1286. (Pubitemid 39129231)
71. Sunaoshi K, et al. 2009. Molecular emm genotyping and antibiotic susceptibility of Streptococcus dysgalactiae subsp. Equisimilis isolated from invasive and non-invasive infections. J Med Microbiol. 59:82-88.
72. Suzuki H, Brown CJ, Forney LJ, Top EM. 2008. Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Res. 15:357-365.
73. Takahashi T, et al. 2010. Clinical aspects of invasive infection with Streptococcus dysgalactiae subsp. equisimilis in elderly patients. J Infect Chemother. 16:68-71.
74. Talkington DF, et al. 1993. Association of phenotypic and genotypic characteristics of invasive Streptococcus pyogenes isolates with clinical components of streptococcal toxic shock syndrome. Infect Immun. 61:3369-3374. (Pubitemid 23223428)
75. Tanaka D, et al. 2008. Genetic features of clinical isolates of Streptococcus dysgalactiae subsp. equisimilis possessing Lancefield's group A antigen. J Clin Microbiol. 46:1526-1529. (Pubitemid 351563609)
76. Torgerson DG, et al. 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet 5:e1000592.
77. Touchon M, Rocha EP. 2008. From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie 90:648-659.
78. Vieira VV, et al. 1998. Genetic relationships among the different phenotypes of Streptococcus dysgalactiae strains. Int J Syst Bacteriol. 48(Pt 4):1231-1243. (Pubitemid 28523336)
79. Wray GA, et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 20:1377-1419. (Pubitemid 37086669)
80. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)
81. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821-829. (Pubitemid 351645072)
82. Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479. (Pubitemid 41661383)
83. Zhao J, et al. 2007. Cloning, expression, and characterization of the superantigen streptococcal pyrogenic exotoxin G from Streptococcus dysgalactiae. Infect Immun. 75:1721-1729. (Pubitemid 46559437)
84. Zhu H, Liu M, Sumby P, Lei B. 2009. The secreted esterase of group a streptococcus is important for invasive skin infection and dissemination in mice. Infect Immun. 77:5225-5232.